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- EMDB-8633: CryoEM Structure of a Prokaryotic Cyclic Nucleotide-Gated Ion Channel -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-8633 | |||||||||
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Title | CryoEM Structure of a Prokaryotic Cyclic Nucleotide-Gated Ion Channel | |||||||||
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Function / homology | ![]() HCN channel complex / regulation of membrane depolarization / voltage-gated potassium channel activity / sodium ion transmembrane transport Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||
![]() | James ZM / Borst AJ / Haitin Y / Frenz B / DiMaio F / Zagotta WN / Veesler D | |||||||||
![]() | ![]() Title: CryoEM structure of a prokaryotic cyclic nucleotide-gated ion channel. Authors: Zachary M James / Andrew J Borst / Yoni Haitin / Brandon Frenz / Frank DiMaio / William N Zagotta / David Veesler / ![]() ![]() Abstract: Cyclic nucleotide-gated (CNG) and hyperpolarization-activated cyclic nucleotide-regulated (HCN) ion channels play crucial physiological roles in phototransduction, olfaction, and cardiac pace making. ...Cyclic nucleotide-gated (CNG) and hyperpolarization-activated cyclic nucleotide-regulated (HCN) ion channels play crucial physiological roles in phototransduction, olfaction, and cardiac pace making. These channels are characterized by the presence of a carboxyl-terminal cyclic nucleotide-binding domain (CNBD) that connects to the channel pore via a C-linker domain. Although cyclic nucleotide binding has been shown to promote CNG and HCN channel opening, the precise mechanism underlying gating remains poorly understood. Here we used cryoEM to determine the structure of the intact LliK CNG channel isolated from -which shares sequence similarity to eukaryotic CNG and HCN channels-in the presence of a saturating concentration of cAMP. A short S4-S5 linker connects nearby voltage-sensing and pore domains to produce a non-domain-swapped transmembrane architecture, which appears to be a hallmark of this channel family. We also observe major conformational changes of the LliK C-linkers and CNBDs relative to the crystal structures of isolated C-linker/CNBD fragments and the cryoEM structures of related CNG, HCN, and KCNH channels. The conformation of our LliK structure may represent a functional state of this channel family not captured in previous studies. | |||||||||
History |
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Structure visualization
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 33.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13.2 KB 13.2 KB | Display Display | ![]() |
Images | ![]() | 65.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 407.3 KB | Display | ![]() |
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Full document | ![]() | 406.8 KB | Display | |
Data in XML | ![]() | 6 KB | Display | |
Data in CIF | ![]() | 6.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5v4sMC ![]() 8632C C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Unsharpened map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.3655 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : LliK
Entire | Name: LliK |
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Components |
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-Supramolecule #1: LliK
Supramolecule | Name: LliK / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
Molecular weight | Theoretical: 200 KDa |
-Macromolecule #1: LliK
Macromolecule | Name: LliK / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MKHHHHHHHH PMSDVDIPTT ENLYFQGSGS MGITLKNRIR VYWDILVFIC IFWASLESPL RIVINYDPNL LLTCIYFFID FVFALDIL W NCFTPEYKDG KWILTRSQVI KDYLGSWFII DLIAALPLEY ATTTIFGLQQ SQYPYLYLLL GVTRILKVFR ISDILQRINL ...String: MKHHHHHHHH PMSDVDIPTT ENLYFQGSGS MGITLKNRIR VYWDILVFIC IFWASLESPL RIVINYDPNL LLTCIYFFID FVFALDIL W NCFTPEYKDG KWILTRSQVI KDYLGSWFII DLIAALPLEY ATTTIFGLQQ SQYPYLYLLL GVTRILKVFR ISDILQRINL AFQPTPGI L RLVLFAFWAT LVAHWCAVGW LYVDDLLDYQ TGWSEYIIAL YWTVATIATV GYGDITPSTD SQRIYTIFVM ILGAGVYATV IGNIASIL G SLDLAKAAQR KKMAQVDSFL KARNISQNIR RRVRDYYMYI IDRGWGEDEN ALLNDLPISL RREVKIQLHR DLLEKVPFLK GADPALVT S LVFSMKPMIF LEGDTIFRRG EKGDDLYILS EGSVDILDSD EKTILLSLQE GQFFGELALV MDAPRSATVR ATTTCEIYTL SKTDFDNVLK RFSQFRSAIE ESVAHLKKR |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.9 mg/mL | ||||||||||||||||||
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Buffer | pH: 7.9 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.4 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: OTHER |
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Output model | ![]() PDB-5v4s: |